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- PDB-1ysm: NMR Structure of N-terminal domain (Residues 1-77) of Siah-Intera... -

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Basic information

Entry
Database: PDB / ID: 1ysm
TitleNMR Structure of N-terminal domain (Residues 1-77) of Siah-Interacting Protein.
ComponentsCalcyclin-binding protein
KeywordsMETAL BINDING PROTEIN / helix-turn-helix
Function / homology
Function and homology information


cardiac muscle cell differentiation / beta-catenin destruction complex / S100 protein binding / response to growth hormone / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / heart development ...cardiac muscle cell differentiation / beta-catenin destruction complex / S100 protein binding / response to growth hormone / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / heart development / cell body / molecular adaptor activity / protein domain specific binding / ubiquitin protein ligase binding / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / UVR domain / SGS domain / SGS domain / SGS domain profile. / DNA Excision Repair, Uvrb; Chain A ...Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / : / Siah interacting protein, N terminal / UVR domain / SGS domain / SGS domain / SGS domain profile. / DNA Excision Repair, Uvrb; Chain A / CS domain / CS domain / CS domain profile. / HSP20-like chaperone / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Calcyclin-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Torsion Angle Dynamics Simulated Annealing Restrained Molecular Dynamics
AuthorsBhattacharya, S. / Lee, Y.T. / Michowski, W. / Jastrzebska, B. / Filipek, A. / Kuznicki, J. / Chazin, W.J.
CitationJournal: Biochemistry / Year: 2005
Title: The Modular Structure of SIP Facilitates Its Role in Stabilizing Multiprotein Assemblies.
Authors: Bhattacharya, S. / Lee, Y.T. / Michowski, W. / Jastrzebska, B. / Filipek, A. / Kuznicki, J. / Chazin, W.J.
History
DepositionFeb 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcyclin-binding protein


Theoretical massNumber of molelcules
Total (without water)8,7871
Polymers8,7871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with favorable non-bond energy, least restraint violations and lowest energy
RepresentativeModel #2closest to the average

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Components

#1: Protein Calcyclin-binding protein / CacyBP / Siah-interacting protein / SIP


Mass: 8787.200 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cacybp, Sip / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CXW3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1243D 13C-separated NOESY
1314D 13C/15N-separated NOESY
1444D 13C-separated NOESY
152HNHA
162HNHB
1743D-HACAHB-COSY
NMR detailsText: Stereospecific methyl group assignments were made with 10% 13C-enriched SIP(1-77) sample.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 15N/13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl90% H2O/10% D2O
21 mM 15N-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl90% H2O/10% D2O
31 mM U-SIP(1-77), 20 mM NaPi, 50 mM NaCl90% H2O/10% D2O
41 mM 13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl100% D2O
51 mM 10% 13C-enriched SIP(1-77), 20 mM NaPi, 50 mM NaCl100% D2O
61 mM U-SIP(1-77), 20 mM NaPi, 50 mM NaCl100% D2O
Sample conditionsIonic strength: 20 mM NaPi, 50 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Felix2000Accelrysprocessing
SANE1Duggan, B. M.data analysis
DYANA1.5Guntert, P.structure solution
Amber7Pearlman, D. A.refinement
RefinementMethod: Torsion Angle Dynamics Simulated Annealing Restrained Molecular Dynamics
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, least restraint violations and lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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